RecName: Full=Bifunctional lycopene cyclase/phytoene synthase; Includes: RecName: Full=Lycopene beta-cyclase; AltName: Full=Lycopene cyclase; Includes: RecName: Full=Phytoene synthase
Protein Classification
phytoene/squalene synthase family protein( domain architecture ID 10022455)
phytoene/squalene synthase family protein catalyzes the head-to-head condensation of two isoprenyl diphosphates, such as phytoene synthase that catalyzes the condensation of two molecules of geranylgeranyl diphosphate (GGPP) to give prephytoene diphosphate (PPPP) and the subsequent rearrangement of the cyclopropylcarbinyl intermediate to yield phytoene
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| Trans_IPPS_HH | cd00683 | Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ... |
293-572 | 7.36e-66 | |||||
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea. : Pssm-ID: 173831 [Multi-domain] Cd Length: 265 Bit Score: 215.56 E-value: 7.36e-66
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| CarR_dom_SF | TIGR03462 | lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as ... |
3-94 | 2.30e-19 | |||||
lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. : Pssm-ID: 274590 Cd Length: 89 Bit Score: 83.03 E-value: 2.30e-19
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| CarR_dom_SF | TIGR03462 | lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as ... |
147-237 | 2.69e-14 | |||||
lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. : Pssm-ID: 274590 Cd Length: 89 Bit Score: 68.40 E-value: 2.69e-14
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| Name | Accession | Description | Interval | E-value | |||||
| Trans_IPPS_HH | cd00683 | Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ... |
293-572 | 7.36e-66 | |||||
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea. Pssm-ID: 173831 [Multi-domain] Cd Length: 265 Bit Score: 215.56 E-value: 7.36e-66
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| SQS_PSY | pfam00494 | Squalene/phytoene synthase; |
293-571 | 2.18e-65 | |||||
Squalene/phytoene synthase; Pssm-ID: 425717 [Multi-domain] Cd Length: 261 Bit Score: 214.46 E-value: 2.18e-65
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| ERG9 | COG1562 | Phytoene/squalene synthetase [Lipid transport and metabolism]; |
293-580 | 9.27e-61 | |||||
Phytoene/squalene synthetase [Lipid transport and metabolism]; Pssm-ID: 441170 [Multi-domain] Cd Length: 278 Bit Score: 202.73 E-value: 9.27e-61
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| HpnD | TIGR03465 | squalene synthase HpnD; The genes of this family are often found in the same genetic locus ... |
294-580 | 6.34e-34 | |||||
squalene synthase HpnD; The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. Pssm-ID: 163278 Cd Length: 266 Bit Score: 129.71 E-value: 6.34e-34
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| PLN02632 | PLN02632 | phytoene synthase |
285-578 | 2.02e-28 | |||||
phytoene synthase Pssm-ID: 215339 Cd Length: 334 Bit Score: 115.97 E-value: 2.02e-28
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| CarR_dom_SF | TIGR03462 | lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as ... |
3-94 | 2.30e-19 | |||||
lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. Pssm-ID: 274590 Cd Length: 89 Bit Score: 83.03 E-value: 2.30e-19
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| CarR_dom_SF | TIGR03462 | lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as ... |
147-237 | 2.69e-14 | |||||
lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. Pssm-ID: 274590 Cd Length: 89 Bit Score: 68.40 E-value: 2.69e-14
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| Name | Accession | Description | Interval | E-value | |||||
| Trans_IPPS_HH | cd00683 | Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate ... |
293-572 | 7.36e-66 | |||||
Trans-Isoprenyl Diphosphate Synthases, head-to-head; These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea. Pssm-ID: 173831 [Multi-domain] Cd Length: 265 Bit Score: 215.56 E-value: 7.36e-66
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| SQS_PSY | pfam00494 | Squalene/phytoene synthase; |
293-571 | 2.18e-65 | |||||
Squalene/phytoene synthase; Pssm-ID: 425717 [Multi-domain] Cd Length: 261 Bit Score: 214.46 E-value: 2.18e-65
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| ERG9 | COG1562 | Phytoene/squalene synthetase [Lipid transport and metabolism]; |
293-580 | 9.27e-61 | |||||
Phytoene/squalene synthetase [Lipid transport and metabolism]; Pssm-ID: 441170 [Multi-domain] Cd Length: 278 Bit Score: 202.73 E-value: 9.27e-61
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| HpnD | TIGR03465 | squalene synthase HpnD; The genes of this family are often found in the same genetic locus ... |
294-580 | 6.34e-34 | |||||
squalene synthase HpnD; The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. Pssm-ID: 163278 Cd Length: 266 Bit Score: 129.71 E-value: 6.34e-34
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| PLN02632 | PLN02632 | phytoene synthase |
285-578 | 2.02e-28 | |||||
phytoene synthase Pssm-ID: 215339 Cd Length: 334 Bit Score: 115.97 E-value: 2.02e-28
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| Trans_IPPS | cd00867 | Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of ... |
299-548 | 1.80e-24 | |||||
Trans-Isoprenyl Diphosphate Synthases; Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Mechanistically and structurally distinct, cis-IPPS are not included in this CD. Pssm-ID: 173836 Cd Length: 236 Bit Score: 102.04 E-value: 1.80e-24
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| Isoprenoid_Biosyn_C1 | cd00385 | Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases ... |
299-546 | 3.89e-24 | |||||
Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD. Pssm-ID: 173830 [Multi-domain] Cd Length: 243 Bit Score: 101.42 E-value: 3.89e-24
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| HpnC | TIGR03464 | squalene synthase HpnC; This family of genes are members of a superfamily (pfam00494) of ... |
300-580 | 2.01e-22 | |||||
squalene synthase HpnC; This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnD gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. Pssm-ID: 274592 [Multi-domain] Cd Length: 266 Bit Score: 96.98 E-value: 2.01e-22
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| CarR_dom_SF | TIGR03462 | lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as ... |
3-94 | 2.30e-19 | |||||
lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. Pssm-ID: 274590 Cd Length: 89 Bit Score: 83.03 E-value: 2.30e-19
|
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| CarR_dom_SF | TIGR03462 | lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as ... |
147-237 | 2.69e-14 | |||||
lycopene cyclase domain; This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. Pssm-ID: 274590 Cd Length: 89 Bit Score: 68.40 E-value: 2.69e-14
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| squal_synth | TIGR01559 | farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate ... |
293-483 | 6.20e-04 | |||||
farnesyl-diphosphate farnesyltransferase; This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family. Pssm-ID: 188157 Cd Length: 337 Bit Score: 42.43 E-value: 6.20e-04
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